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At least 649 records · Page 36Linked to original sources
PubMed2002

High resolution mapping of quantitative trait loci by linkage disequilibrium analysis.

Two methods, linkage analysis and linkage disequilibrium (LD) mapping or association study, are usually utilised for mapping quantitative trait loci (QTL). Linkage mapping is appropriate for low resolution mapping to localise trait loci to broad chromosome regions within a few cM (<10 cM), and is based on family data. Linkage disequilibrium mapping, on the other hand, is useful in high resolution or fine mapping, and is based on both population and family data. Using only one marker, one may carry out single-point linkage analysis and linkage disequilibrium mapping. Using two or more markers, it is possible to flank the QTL by multipoint analysis. The development and thus availability of dense marker maps, such as single nucleotide polymorphisms (SNP) in human genome, presents a tremendous opportunity for multipoint fine mapping. In this article, we propose a regression approach of mapping QTL by linkage disequilibrium mapping based on population data. Assuming that two marker loci flank one quantitative trait locus, a two-point linear regression is proposed to analyse population data. We derive analytical formulas of parameter estimations, and non-centrality parameters of appropriate tests of genetic effects and linkage disequilibrium coefficients. The merit of the method is shown by the power calculation and comparison. The two-point regression model can capture much more linkage and linkage disequilibrium information than that derived when only one marker is used. For a complex disease with heritability h(2)> or =0.15, a study with sample size of 250 can provide high power for QTL detection under moderate linkage disequilibria.

Chromosome Mapping↗
PubMed2005

ASAP, a human microtubule-associated protein required for bipolar spindle assembly and cytokinesis.

We have identified a unique human microtubule-associated protein (MAP) named ASAP for ASter-Associated Protein. ASAP localizes to microtubules in interphase, associates with the mitotic spindle during mitosis, localizes to the central body during cytokinesis and directly binds to purified microtubules by its COOH-terminal domain. Overexpression of ASAP induces profound bundling of cytoplasmic microtubules in interphase cells and aberrant monopolar spindles in mitosis. Depletion of ASAP by RNA interference results in severe mitotic defects: it provokes aberrant mitotic spindle, delays mitotic progression, and leads to defective cytokinesis or cell death. These results suggest a crucial role for ASAP in the organization of the bipolar mitotic spindle, mitosis progression, and cytokinesis and define ASAP as a key factor for proper spindle assembly.

Base Sequence↗
PubMed2004

Genetic analysis of macrophage characteristics as a tool to identify tumor susceptibility genes: mapping of three macrophage-associated risk inflammatory factors, marif1, marif2, and marif3.

Genetic predisposition to cancer is influenced by allelic variation in tumor susceptibility genes (TSGs) as present in the germline. We previously demonstrated in the mouse that TSGs frequently participate in genetic interactions, indicating that they represent molecular networks. Inflammation may constitute one of the molecular networks underlying susceptibility to cancer by influencing the tumor microenvironment. Because macrophages play a key role in inflammation and are often associated with tumors, we argue that a subset of TSGs can be identified by examining the genetics of macrophage characteristics. A panel of inflammation-related assays was established to phenotype mouse bone marrow-derived macrophages, which included stimulation with lipopolysaccharides followed by measurement of secretion of tumor necrosis factor alpha and the p40 chain of interleukin-12 and of expression of inducible nitric oxide synthase and cyclooxygenase-2. This panel of assays was used for linkage analysis and applied to bone marrow-derived macrophages derived from individual mice of segregating crosses between inbred strain O20 and the highly related strains NTX-10 and NTX-20, which differed from O20 in only 10% of their genome, to reduce genetic complexity. Three macrophage-associated risk inflammatory factors were mapped-Marif1, Marif2, and Marif3-that each affected several inflammation-related assays, confirming that they function within molecular networks. Moreover, Marif1 and Marif2 were localized in regions with established linkage for both quantitative and qualitative aspects of lung cancer susceptibility. These studies provide a novel approach to investigate the genetics of microenvironmental influence on predisposition to tumorigenesis, thereby contributing to development of new strategies that aim to prevent or treat cancer.

Animals↗
PubMed2006

Cytokine responses of bovine macrophages to diverse clinical Mycobacterium avium subspecies paratuberculosis strains.

BACKGROUND: Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease (JD) persistently infects and survives within the host macrophages. While it is established that substantial genotypic variation exists among MAP, evidence for the correlates that associate specific MAP genotypes with clinical or sub-clinical disease phenotypes is presently unknown. Thus we studied strain differences in intracellular MAP survival and host responses in a bovine monocyte derived macrophage (MDM) system. RESULTS: Intracellular survival studies showed that a bovine MAP isolate (B1018) and a human MAP isolate (Hu6) persisted in relatively higher numbers when compared with a sheep MAP isolate (S7565) at 24-hr, 48-hr and 96-hr post infection (PI). MDMs stimulated with B1018 up-regulated IL-10 at the transcript level and down-regulated TNFalpha at the protein and transcript levels compared with stimulations by the S7565 and Hu6. MDMs infected with Hu6 showed a down regulatory pattern of IL-10 and TNFalpha compared to stimulations by S7565. Cells stimulated with B1018 and Hu6 had low levels of matrix metalloprotease-3 (MMP3) and high levels of tissue inhibitor of metalloprotease-1 (TIMP1) at 96-hr PI relative to MDMs stimulated by S7565. CONCLUSION: Taken together, results suggest that the bovine (B1018) and the human (Hu6) MAP isolates lead to anti-inflammatory and anti-invasive pathways in the macrophage environment whereas the sheep (S7565) MAP isolate induces a pro-inflammatory pathway. Thus the infecting strain genotype may play a role in polarizing the host immune responses and dictate the clinicopathological outcomes in this economically important disease.

Animals↗
PubMed1983

Characterisation of microtubule-associated proteins at the synapse: absence of MAP 2.

The high molecular weight microtubule-associated proteins MAP 1 and MAP 2 are major components of brain cytosol and can be readily identified using polyacrylamide gel electrophoresis on the basis of heat-stability and co-sedimentation with microtubules. An examination of synaptosomal cytosol, synaptic plasma membrane and postsynaptic density fractions showed that MAP 2 is absent from these fractions and thus from both pre- and postsynaptic sites. All of the fractions contained polypeptides that comigrated with MAP 1 and a MAP 1 like polypeptide was identified in a microtubule preparation from synaptosomal cytosol. The absence of MAP 2 from synaptosomal cytosol was confirmed by immunoblotting using an antibody directed against MAP 2. Immunocytochemistry using this antibody showed that MAP 2 was present in cell bodies and dendrites but absent from axons.

Animals↗
PubMed2005

Cross correlation maps: a tool for visualizing and modeling time lagged associations.

It has long been recognized that arthropod populations fluctuate with changes in environmental conditions and these changes occur at various spatial and temporal scales. Empirical studies that have explored associations between vector abundance and the environment often considered meterological events as leading indicators with their effects traditionally restricted to single points in time, such as precipitation 12 days prior to trapping. Field experience, however, suggests that the duration of these environmental effects on vectors often extends over a range or interval of time. Such a scenario is not directly interpretable from cross correlation plots routinely employed to visualize and identify time lag associations. Cross correlation maps are introduced as a way to generalize cross correlation plots and to visualize the effects of environmental conditions over intervals of time. This graphical method is flexible and can include different characterizations of environmental effects, as well as interactions among environmental variables. A time series of daily trapped female Ochlerotatus sollicitans mosquitos and leading meterologic conditions were used for demonstration. Associations shown in cross correlation maps were consistent with the arthropod biology and trapping efficacy and were also stronger than those identified at single time points using cross correlation plots. Poisson regression models for vector abundance built using meterological variables with both single and interval based leading time lags were compared. The approach based on the leading meterological events allowed to extend over time intervals reproduced the Oc. sollicitans daily population dynamics better than the traditional approach.

Animals↗
PubMed1991

Physical mapping of virulence-associated genes in Pseudomonas aeruginosa by transverse alternating-field electrophoresis.

The relative chromosomal locations of 20 virulence-associated genes in four clinical isolates of Pseudomonas aeruginosa were investigated by using transverse alternating-field electrophoresis. Each strain had a characteristic restriction pattern when digested with either SpeI or DraI and electrophoresed with 15-s pulses. All four strains had restriction fragments that hybridized with each of the gene probes used, although there were variations in fragment size. An SpeI physical map constructed by Ratnaningsih et al. (E. Ratnaningsih, S. Dharmsthiti, V. Krishnapillai, A. Morgan, M. Sinclair, and B. W. Holloway, J. Gen. Microbiol. 136:2351-2357, 1990) for one of these strains, PAO1, was used to identify the location of 11 previously unmapped genes. The physical locations of the remaining genes were found to be consistent with their genetically mapped loci. Whereas phospholipase C and alginate structural and regulatory genes were associated in three separate clusters in the early, middle, and late regions of the chromosome, no virulence cluster was identified. Our data suggest that the pathogenicity of P. aeruginosa results from the gradual acquisition of genes encoding various virulence determinants.

Blotting, Southern↗
PubMed2005

A multi-perspective concept mapping study of problems associated with traumatic brain injury.

OBJECTIVE: To develop a model of the problems of persons with traumatic brain injury that includes multiple perspectives as well as the multi-dimensional nature of the phenomena. DESIGN: Concept mapping, a multi-variate modelling strategy, was employed to produce an exhaustive inventory and concept map of TBI-related problems based on input from patients, family caregivers and professional providers. RESULTS: The eight-cluster concept map included the following dimensions: social competence, intimacy, behavioural, maturity/independence, neurophysiological, mood, executive functions and non-executive functions. CONCLUSIONS: An underlying two-dimensional conceptual model of TBI problems is proposed with relevance for theory, practice and further research.

Adult↗
PubMed1993

Primary endocrine therapy for advanced breast cancer: to start with tamoxifen or with medroxyprogesterone acetate?

BACKGROUND: The availability of compounds effective against metastatic disease and at the same time excellently tolerated even in long-term administration has determined the choice of tamoxifen as primary treatment for palliation in metastatic breast cancer. Other drugs or other hormonal approaches were hardly tested against tamoxifen, especially as first-line treatment. PATIENTS AND METHODS: 119 patients with metastatic breast cancer and no prior endocrine therapy were randomized to receive either tamoxifen (TAM) 20 mg/day orally (64 patients), or medroxyprogesterone acetate (MAP) 1g/day i.m. 5 days/week for 4 weeks and then 500 mg twice a week (55 patients). The subsequent endocrine therapy was also prospectively defined at study entry. RESULTS: A total of 111 events, contributing to the endpoint 'time to progression' have so far been observed: a study of similar size would have a 90% power to detect a hazard ratio of 1.85. Initial MAP was associated with a significantly higher remission rate (50% versus 30% for tamoxifen; p = 0.023) and a marginally significantly longer median time to progression (8.8 versus 5.4 months; p = 0.051). Overall survival was also longer for the MAP group (28 versus 20 months; p = 0.384). The use of MAP was associated with a significantly higher toxicity, mainly hypertension, weight gain and tremor. CONCLUSIONS: The implications of these results are that initial endocrine therapy in postmenopausal patients with metastatic disease should be MAP if the patient is willing to accept the side effects of high-dose progestins. Progestins should be tested in the adjuvant setting for postmenopausal women, especially those with no tendency to hypertension or obesity.

Adult↗
PubMed1996

Microinjection of intact MAP-4 and fragments induces changes of the cytoskeleton in PtK2 cells.

The molecular cloning and sequencing of microtubule-associated protein (MAP)-4 identified microtubule-binding repeats near the C-terminus and a projection domain near the N-terminus. Although it is well known that MAP-4 stimulates the assembly of and stabilizes microtubules (MT) in vitro, the function of MAP-4 in vivo is still unclear. In this study, we examined the function of MAP-4 in the cytoskeleton both in vitro and in vivo. Intact MAP-4 was prepared from bovine adrenal cortex, and the truncated fragments of the N- and the C-terminal halves (named NR and PA4 fragments, respectively) were expressed in Escherichia coli and isolated. In vitro studies demonstrated that in a solution containing a physiological concentration of NaCl, intact MAP-4 and the PA4 fragment were bound to MT, but not to F-actin. The NR fragment was not bound to MT or to F-actin. We also examined the MT changes in PtK2 cells after they had been microinjected with intact MAP-4 and the truncated fragments of PA4 and NR. The injection of intact MAP-4 or PA4 into the cells induced an increase in the number of cytoplasmic MT, as well as MT bundling. The NR fragment did not affect the MT array. Injected MAP-4 and PA4 were associated with the increased MT. In addition, injection with MAP-4 and PA4 stabilized MT in relation to treatment with the MT-disrupting drug, nocodazole. These results indicated that intact MAP-4 and the PA4 fragment promoted MT assembly and stabilized MT, by binding to MT, in vivo as well as in vitro. Further, the injection of the PA4 fragment induced an increase in stress fibers. However, these proteins did not show any association with the stress fibers. Our results suggest that there is an indirect effect of MAP-4 on stress fibers rather than a direct interaction between MAP-4 and stress fibers.

Actins↗
PubMedDate not supplied

The c-Ha-ras1, insulin and beta-globin loci map outside the deletion associated with aniridia-Wilms' tumour.

The localization of protooncogenes on human chromosomes may coincide with chromosome breakpoints of consistent translocations in leukaemias or lymphomas, suggesting a direct involvement of oncogenes in carcinogenesis. For example, in Burkitt's lymphoma consistent translocations may be associated with rearrangements of c-myc. Our assignment of the c-Harvey-ras1 oncogene to chromosome 11, precisely to region 11p11 leads to p15 (ref. 5; not 11p13 as stated in ref. 6), has raised the possibility that this oncogene might have a role in the predisposition to nephroblastoma (Wilms' tumour, WT) seen in the aniridia-WT association (AWTA) that is frequently caused by an interstitial deletion of band 11p (ref. 8). We have now studied the organization and copy number of sequences at three loci mapped to 11p: c-Ha-ras1, insulin and gamma-globin in cells from four individuals with structural rearrangements of the short arm of chromosome 11. Our results reported here rule out a close physical linkage between c-Ha-ras1 and the genes responsible for AWTA, and suggest a more distal localization of the beta-globin cluster than currently assumed.

Alleles↗
PubMed1998

Genetics of complex human diseases: genome screening, association studies and fine mapping.

Positional cloning has been applied successfully to many Mendelian disorders. Because of the public health significance, there is strong interest in mapping susceptibility genes for common disorders, such as asthma and allergy, that have a genetic component. Genome-wide screening has been very useful in detecting regions of the genome likely to contain susceptibility genes. There are multiple chromosomal regions implicated in asthma and now the difficult process of finding the genes and relevant mutations is underway. Two approaches that are being utilized are those of association studies in candidate genes, and haplotype sharing or identical by descent (IBD) mapping. Although these are useful approaches, it is important to realize the strengths and limitations of each. The level of significance needed for an initial study or a replication study should be considered in light of the prior evidence for studying a specific gene polymorphism. Haplotype-sharing approaches, although difficult to use in outbred heterogeneous populations, may provide important insight into fine mapping and gene localization.

Asthma↗
PubMed2004

In silico fine-mapping: narrowing disease-associated loci by intergenomics.

UNLABELLED: Genetic linkage and association studies define quantitative trait loci (QTLs) and susceptibility loci (SLs) that influence the phenotype of polygenic traits. A web-accessible application was created to identify intergenomic consensuses to fine map QTLs and SLs in silico and select particularly promising candidate genes for such traits. Furthermore, this approach offers an empirical evaluation of animal models for their applicability to the study of human traits. AVAILABILITY: http://qtl.pzr.uni-rostock.de/qtlmix.php CONTACT: serrano@pzr.uni-rostock.de.

Animals↗